Contacts of the strand formed by residues 34 - 42 (chain G) in PDB entry 4UN7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 34 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G LEU 3.5 11.7 - - - -
28G LYS* 5.3 1.3 - - - -
29G TYR* 4.4 3.8 - - - -
32G ASN 3.8 1.1 + - - -
33G ARG* 1.3 78.2 - - - +
35G GLU* 1.3 66.9 + - - +
36G TYR* 3.5 10.1 - - - -
3I C 4.4 3.8 - - - -
4I G 2.6 52.1 + - - -
5I C 3.1 24.7 + - - -
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Residues in contact with GLU 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G TYR 3.8 0.2 - - - +
26G LYS* 3.7 0.9 - - - +
27G LEU* 2.8 34.4 + - + +
29G TYR* 2.5 35.9 + - + +
34G SER* 1.3 79.5 - - - +
36G TYR* 1.3 75.8 + - - +
37G ARG* 3.0 30.5 + - + +
70G GLN* 5.0 0.3 + - - -
81G ARG* 4.8 1.4 - - - -
83G SER* 2.5 32.3 + - - +
4I G 4.8 1.3 - - - -
5I C 3.9 10.5 - - + +
6I C 2.9 31.0 + - - -
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Residues in contact with TYR 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G TYR 3.3 4.3 - - - -
26G LYS* 3.7 32.7 - - + +
34G SER* 3.5 22.3 - - - -
35G GLU* 1.3 81.0 - - - +
37G ARG* 1.3 61.0 + - - +
82G VAL 3.7 0.2 - - - +
83G SER* 3.5 5.4 + - - -
84G SER 2.9 28.2 + - - +
85G LYS* 3.6 54.8 - - + -
88G TYR* 3.6 31.6 - + + -
89G TYR* 4.0 13.4 + + - -
4I G 2.7 31.0 + - + -
5I C 4.0 7.1 + - - -
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Residues in contact with ARG 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G GLY 3.8 0.2 - - - +
24G LEU* 3.4 6.8 - - - -
25G TYR* 2.7 41.9 + - + +
27G LEU* 3.9 11.9 - - + -
29G TYR* 3.5 8.7 + - - -
35G GLU* 3.0 37.8 + - - +
36G TYR* 1.3 76.9 - - - +
38G VAL* 1.3 60.9 + - - +
39G VAL* 3.8 19.1 - - + -
79G GLU* 5.0 0.6 + - - -
81G ARG* 3.2 46.6 - - + +
82G VAL 3.6 2.7 - - - +
83G SER* 4.5 1.3 - - - +
88G TYR* 3.8 6.1 - - - -
17H T 3.6 18.1 + - - +
18H C 3.6 4.0 - - - +
7I G 2.8 29.9 + - - -
8I G 2.5 24.2 + - - -
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Residues in contact with VAL 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ILE* 3.5 32.3 - - + -
23G GLY 3.8 2.9 - - - -
24G LEU* 3.8 9.4 - - + -
37G ARG* 1.3 71.8 - - - +
39G VAL* 1.3 60.3 + - - +
56G MET* 3.9 14.1 - - + -
80G LEU* 3.8 2.4 - - - +
81G ARG* 3.6 3.3 - - - -
82G VAL* 2.9 38.2 + - + +
84G SER 5.0 0.9 - - - +
87G LEU* 3.8 18.4 - - + +
88G TYR* 3.7 35.4 - - + +
91G PHE* 3.7 15.0 - - + -
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Residues in contact with VAL 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ILE* 3.8 5.2 - - - +
22G GLY* 3.4 7.3 - - - -
23G GLY 3.0 31.7 + - - +
25G TYR* 3.7 32.5 - - + -
37G ARG* 3.8 15.9 - - + -
38G VAL* 1.3 76.9 - - - +
40G ILE* 1.3 72.8 + - - +
41G THR* 3.9 15.9 - - + -
79G GLU* 3.3 39.9 - - + +
80G LEU 3.4 3.1 - - - -
81G ARG* 4.6 4.5 - - + -
16H T 4.5 4.3 - - + -
17H T 5.6 0.4 - - + -
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Residues in contact with ILE 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 4.0 6.3 - - + +
17G LEU* 3.6 40.6 - - + +
18G ILE* 3.5 26.2 - - + -
21G ASP* 4.2 5.6 - - + -
22G GLY* 4.2 0.7 - - - -
39G VAL* 1.3 81.7 - - - +
41G THR* 1.3 71.2 + - - +
42G GLN* 4.9 2.2 - - - +
48G ILE* 4.0 3.6 - - + +
52G ILE* 4.2 30.1 - - + -
56G MET* 4.4 17.0 - - + -
79G GLU 3.7 0.2 - - - -
80G LEU* 2.8 46.9 + - + +
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Residues in contact with THR 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ASP* 2.4 35.0 + - - +
22G GLY* 4.8 1.1 - - - -
39G VAL* 3.9 17.9 - - + -
40G ILE* 1.3 78.3 - - - +
42G GLN* 1.3 78.4 + - - +
48G ILE* 4.4 0.2 - - - -
77G ARG* 4.3 15.0 - - - +
78G TYR 3.2 13.0 - - - +
79G GLU* 4.2 10.1 - - + -
14H A 3.3 25.2 - - - +
15H G 4.2 17.3 - - + -
16H T 4.8 1.1 - - + -
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Residues in contact with GLN 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G LEU* 5.7 4.9 - - - +
21G ASP* 2.7 25.7 + - - +
40G ILE* 4.9 2.6 - - - +
41G THR* 1.3 78.2 + - - +
43G LYS* 1.3 65.1 + - - +
44G SER* 3.5 9.8 + - - +
47G LEU* 3.5 34.8 - - + +
48G ILE* 3.7 20.6 - - + +
52G ILE* 4.8 8.2 - - + +
77G ARG* 4.5 2.7 - - - -
78G TYR* 2.8 34.4 + - - +
115G VAL* 5.1 5.6 + - - +
116G ALA* 5.2 2.4 - - - +
1182G ZN 3.7 2.9 - - - -
14H A 2.8 33.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il